Crystal structure of a vFLIP-IKKgamma stapled peptide dimer

Experimental Data Snapshot

  • Resolution: 3.38 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


IKK gamma-Mimetic Peptides Block the Resistance to Apoptosis Associated with Kaposi's Sarcoma-Associated Herpesvirus Infection.

Briggs, L.C.Chan, A.W.E.Davis, C.A.Whitelock, N.Hotiana, H.A.Baratchian, M.Bagneris, C.Selwood, D.L.Collins, M.K.Barrett, T.E.

(2017) J Virol 91

  • DOI: https://doi.org/10.1128/JVI.01170-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Primary effusion lymphoma (PEL) is a lymphogenic disorder associated with Kaposi's sarcoma-associated herpesvirus (KSHV) infection. Key to the survival and proliferation of PEL is the canonical NF-κB pathway, which becomes constitutively activated following overexpression of the viral oncoprotein KSHV vFLIP (ks-vFLIP). This arises from its capacity to form a complex with the modulatory subunit of the IκB kinase (IKK) kinase, IKKγ (or NEMO), resulting in the overproduction of proteins that promote cellular survival and prevent apoptosis, both of which are important drivers of tumorigenesis. Using a combination of cell-based and biophysical assays together with structural techniques, we showed that the observed resistance to cell death is largely independent of autophagy or major death receptor signaling pathways and demonstrated that direct targeting of the ks-vFLIP-IKKγ interaction both in cells and in vitro can be achieved using IKKγ-mimetic peptides. Our results further reveal that these peptides not only induce cell killing but also potently sensitize PEL to the proapoptotic agents tumor necrosis factor alpha and etoposide and are the first to confirm ks-vFLIP as a tractable target for the treatment of PEL and related disorders. IMPORTANCE KSHV vFLIP (ks-vFLIP) has been shown to have a crucial role in cellular transformation, in which it is vital for the survival and proliferation of primary effusion lymphoma (PEL), an aggressive malignancy associated with infection that is resistant to the majority of chemotherapeutic drugs. It operates via subversion of the canonical NF-κB pathway, which requires a physical interaction between ks-vFLIP and the IKK kinase modulatory subunit IKKγ. While this interaction has been directly linked to protection against apoptosis, it is unclear whether the suppression of other cell death pathways implicated in ks-vFLIP pathogenesis is an additional contributor. We demonstrate that the interaction between ks-vFLIP and IKKγ is pivotal in conferring resistance to apoptosis. Additionally, we show that the ks-vFLIP-IKKγ complex can be disrupted using peptides leading to direct killing and the sensitization of PEL cells to proapoptotic agents. Our studies thus provide a framework for future therapeutic interventions.

  • Organizational Affiliation

    Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein G,Viral FLICE protein
A, B
265Streptococcus sp. 'group GHuman gammaherpesvirus 8
This entity is chimeric
Mutation(s): 0 
Gene Names: spgORF71
Find proteins for F5HEZ4 (Human herpesvirus 8 type P (isolate GK18))
Explore F5HEZ4 
Go to UniProtKB:  F5HEZ4
Find proteins for P19909 (Streptococcus sp. group G)
Explore P19909 
Go to UniProtKB:  P19909
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP19909F5HEZ4
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_aC [auth R],
D [auth S]
20Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K9 (Homo sapiens)
Explore Q9Y6K9 
Go to UniProtKB:  Q9Y6K9
GTEx:  ENSG00000269335 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6K9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.38 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.51α = 90
b = 90.51β = 90
c = 134.78γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2017-10-04 
  • Deposition Author(s): Barrett, T.

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC19746/A9867

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 2.0: 2017-11-22
    Changes: Advisory, Atomic model, Database references, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description